Atomistry » Potassium » PDB 3vuw-3zns » 3w1j
Atomistry »
  Potassium »
    PDB 3vuw-3zns »
      3w1j »

Potassium in PDB 3w1j: Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate

Enzymatic activity of Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate

All present enzymatic activity of Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate:
2.9.1.1;

Protein crystallography data

The structure of Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate, PDB code: 3w1j was solved by Y.Itoh, S.Sekine, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.52 / 3.25
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 92.442, 116.372, 124.788, 102.09, 93.39, 106.06
R / Rfree (%) 20 / 26.6

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate (pdb code 3w1j). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate, PDB code: 3w1j:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in 3w1j

Go back to Potassium Binding Sites List in 3w1j
Potassium binding site 1 out of 5 in the Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2001

b:0.2
occ:1.00
 OD1 A:ASP317 2.5 0.3 1.0
OD2 B:ASP317 3.0 90.6 1.0
OD1 A:ASN140 3.2 83.9 1.0
OD1 B:ASN140 3.5 78.5 1.0
CG A:ASP317 3.7 0.9 1.0
CG B:ASP317 3.7 88.6 1.0
CB B:ASP317 3.9 85.8 1.0
OG1 A:THR320 3.9 82.8 1.0
N A:ASP317 4.1 83.5 1.0
CG A:ASN140 4.2 77.6 1.0
CB A:ASP317 4.3 0.7 1.0
N B:ASP317 4.4 75.1 1.0
CG B:ASN140 4.4 72.8 1.0
CG2 A:THR320 4.6 80.1 1.0
O A:ASN140 4.6 74.9 1.0
CA A:ILE316 4.6 79.5 1.0
OD2 A:ASP317 4.6 0.5 1.0
CA A:ASN140 4.7 68.3 1.0
CA B:ASP317 4.7 77.3 1.0
CB A:ASN140 4.8 72.0 1.0
OD1 B:ASP317 4.8 87.4 1.0
CA A:ASP317 4.9 87.9 1.0
CB A:THR320 4.9 80.4 1.0
C A:ILE316 4.9 80.1 1.0
O A:GLN291 4.9 73.6 1.0
CD A:GLN291 4.9 70.4 1.0
NE2 A:GLN291 4.9 84.0 1.0
OG1 B:THR320 4.9 64.2 1.0

Potassium binding site 2 out of 5 in 3w1j

Go back to Potassium Binding Sites List in 3w1j
Potassium binding site 2 out of 5 in the Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K501

b:0.7
occ:1.00
 OD1 D:ASN140 3.0 94.4 1.0
OD1 C:ASN140 3.7 0.6 1.0
OD2 D:ASP317 3.7 0.8 1.0
OG1 D:THR320 3.9 93.0 1.0
CG D:ASN140 3.9 88.4 1.0
OD2 C:ASP317 4.0 0.7 1.0
CB C:ASP317 4.0 0.1 1.0
CG2 D:THR320 4.1 98.6 1.0
CG D:ASP317 4.1 0.0 1.0
O D:ASN140 4.1 88.3 1.0
NE2 D:GLN291 4.2 0.0 1.0
N D:ASP317 4.2 90.9 1.0
CG C:ASP317 4.2 0.7 1.0
CB D:ASN140 4.2 77.3 1.0
CA D:ASN140 4.3 79.1 1.0
OD1 D:ASP317 4.4 0.2 1.0
CA D:ILE316 4.4 90.3 1.0
CG C:ASN140 4.4 92.7 1.0
CB D:THR320 4.5 95.8 1.0
O D:GLN291 4.6 97.9 1.0
C D:ASN140 4.7 87.6 1.0
N C:ASP317 4.7 0.6 1.0
CB D:ILE316 4.8 88.1 1.0
ND2 C:ASN140 4.9 87.6 1.0
C D:ILE316 4.9 88.7 1.0
CB D:ASP317 4.9 0.3 1.0
CD D:GLN291 5.0 0.3 1.0
CA C:ASP317 5.0 0.1 1.0

Potassium binding site 3 out of 5 in 3w1j

Go back to Potassium Binding Sites List in 3w1j
Potassium binding site 3 out of 5 in the Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K501

b:0.9
occ:1.00
 OD1 E:ASN140 3.2 88.5 1.0
OD2 E:ASP317 3.2 0.2 1.0
OD1 F:ASN140 3.5 0.7 1.0
OD2 F:ASP317 3.6 0.4 1.0
OG1 E:THR320 3.8 0.1 1.0
N E:ASP317 3.9 0.9 1.0
CG F:ASP317 4.1 0.6 1.0
CG E:ASN140 4.1 89.2 1.0
CB F:ASP317 4.2 0.3 1.0
CG F:ASN140 4.2 0.2 1.0
CG E:ASP317 4.3 0.2 1.0
CA E:ILE316 4.3 0.2 1.0
CA E:ASN140 4.3 84.1 1.0
CB E:ASN140 4.3 80.6 1.0
CG2 E:THR320 4.3 0.8 1.0
O E:ASN140 4.4 89.0 1.0
CB E:ASP317 4.5 0.7 1.0
C E:ILE316 4.6 98.9 1.0
CB E:ILE316 4.6 0.5 1.0
CB E:THR320 4.7 0.6 1.0
ND2 F:ASN140 4.7 0.1 1.0
N F:ASP317 4.7 0.5 1.0
C E:ASN140 4.8 86.1 1.0
CA E:ASP317 4.8 0.3 1.0
CG2 E:ILE316 4.9 0.6 1.0
O E:GLN291 4.9 0.9 1.0
NE2 E:GLN291 5.0 0.7 1.0

Potassium binding site 4 out of 5 in 3w1j

Go back to Potassium Binding Sites List in 3w1j
Potassium binding site 4 out of 5 in the Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K501

b:0.2
occ:1.00
 OD1 H:ASN140 3.3 0.7 1.0
OD2 H:ASP317 3.3 0.5 1.0
OD2 G:ASP317 3.4 0.1 1.0
OD1 G:ASN140 3.5 0.0 1.0
N H:ASP317 4.0 0.8 1.0
CG H:ASN140 4.0 0.7 1.0
CB H:ASN140 4.0 0.5 1.0
CA H:ASN140 4.1 0.0 1.0
CG G:ASN140 4.2 91.0 1.0
OG1 H:THR320 4.2 0.8 1.0
CG H:ASP317 4.2 0.9 1.0
CG G:ASP317 4.3 0.9 1.0
CB H:ASP317 4.3 0.9 1.0
CA H:ILE316 4.4 0.0 1.0
O H:ASN140 4.4 0.0 1.0
CG2 H:THR320 4.4 0.0 1.0
CB G:ASP317 4.5 0.7 1.0
C H:ASN140 4.7 0.3 1.0
C H:ILE316 4.7 1.0 1.0
CA H:ASP317 4.8 0.8 1.0
CB G:ASN140 4.9 84.0 1.0
N G:ASP317 4.9 0.2 1.0
O H:GLN291 4.9 0.6 1.0
ND2 G:ASN140 4.9 86.5 1.0
CB H:THR320 4.9 0.9 1.0
CB H:ILE316 5.0 0.3 1.0

Potassium binding site 5 out of 5 in 3w1j

Go back to Potassium Binding Sites List in 3w1j
Potassium binding site 5 out of 5 in the Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
I:K501

b:0.1
occ:1.00
 OD2 I:ASP317 3.3 95.1 1.0
OD1 J:ASN140 3.3 89.3 1.0
OD1 I:ASN140 3.4 90.3 1.0
OD2 J:ASP317 3.6 0.5 1.0
OG1 J:THR320 3.7 0.5 1.0
CG J:ASP317 3.8 0.7 1.0
N J:ASP317 3.9 96.6 1.0
CG J:ASN140 4.2 78.4 1.0
OD1 J:ASP317 4.2 0.4 1.0
CA J:ILE316 4.3 83.2 1.0
CG I:ASP317 4.3 93.9 1.0
CB J:ASP317 4.3 0.2 1.0
CG I:ASN140 4.4 82.8 1.0
CA J:ASN140 4.4 59.9 1.0
O J:ASN140 4.4 69.0 1.0
CB I:ASP317 4.4 93.1 1.0
CB J:ASN140 4.5 67.9 1.0
CG2 J:THR320 4.6 0.2 1.0
C J:ILE316 4.6 91.7 1.0
O J:ARG315 4.7 85.7 1.0
CB J:THR320 4.7 0.9 1.0
CA J:ASP317 4.7 0.8 1.0
NE2 I:GLN291 4.9 93.8 1.0
CB J:ILE316 4.9 71.3 1.0
C J:ASN140 4.9 64.3 1.0
O J:GLN291 5.0 82.2 1.0
N I:ASP317 5.0 87.4 1.0

Reference:

Y.Itoh, M.J.Brocker, S.Sekine, G.Hammond, S.Suetsugu, D.Soll, S.Yokoyama. Decameric Sela-Trna(Sec) Ring Structure Reveals Mechanism of Bacterial Selenocysteine Formation Science V. 340 75 2013.
ISSN: ISSN 0036-8075
PubMed: 23559248
DOI: 10.1126/SCIENCE.1229521
Page generated: Mon Aug 12 09:50:12 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy